From: Joel Tyndall <joel.tyndall@ot...> - 2005-06-26 23:00:39
Been sitting here getting a little confused with the seemingly endless
possibilities of the fit and align commands. What I want to do is a
pairwise alignment of the ca atoms of protein portion of some HIV
complexes ie 2 chains of 99 residues).
When I use the command
align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
pinched from robert campbells website (ta) I get the following results:
Match: read scoring matrix.
Match: assigning 208 x 209 pairwise scores.
MatchAlign: aligning residues (208 vs 209)...
ExecutiveAlign: 195 atoms aligned.
ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=2.49).
ExecutiveRMS: 6 atoms rejected during cycle 2 (RMS=0.67).
Executive: RMS = 0.475 (184 to 184 atoms)
I know how to turn off the refinement so thats and that aligns 195 atoms
without refinement. (This can be also complicated when the 2 chains are
A and B or 1-99 and 101-199). So what I am after is the protein
alignment which will align 198 atoms (2 x chain of 99 residues) to give
me a pairwise alignment to compare _multiple _structures.
Could someone point me in the right direction please.
Joel Tyndall, PhD
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
I'm using macPyMOL 0.99rc1 and found very useful the commands
align&pair_fit to do superposition. I'm just wondering which specific
algorithm they use, if somebody never used them to do superposition
of Ca trace for publications, and if there is a specific reference to
Thanks in advance,
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1116
Chicago, IL 60607 - U.S.A.
Tel (312) 996-6299
Fax (312) 355-4535
you can set the number of cycles of refinement on the command line.
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0
I forget what the first 0 means; the second means "don't refine." It'll
use all matching atoms this way.